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Small Intestinal Bacterial Overgrowth

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Last Update: July 18, 2021.

Continuing Education Activity

In contrast to the large intestine, the concentration of the bacteria in the small intestine rarely exceeds 1000 organisms/mL. Gastric acid secretion and intestinal motility limit the overgrowth of bacteria in the small intestine. When these protective mechanisms against excessive bacterial growth fail, small intestinal bacterial overgrowth (SIBO) can manifest. This activity reviews the evaluation and management of hairy cell leukemia and explains the role of the interprofessional team in improving care for patients with this condition.


  • Identify the etiology of small intestinal bacterial overgrowth.
  • Review the appropriate steps to evaluate a patient with suspected small intestinal bacterial overgrowth (SIBO).
  • Outline the treatment and management options available for small intestinal bacterial overgrowth.
  • Discuss interprofessional team strategies for improving care coordination and communication to improve outcomes in patients who present with small intestinal bacterial overgrowth.
Access free multiple choice questions on this topic.


In contrast to the large intestine, the concentration of the bacteria in the small intestine rarely exceeds 1,000 organisms/mL.[1] Gastric acid secretion and intestinal motility limit the overgrowth of bacteria in the small intestine. When these protective mechanisms against excessive bacterial growth fail, small intestinal bacterial overgrowth (SIBO) can manifest. SIBO refers to a condition in which excess bacteria in the small intestine produces intestinal symptoms.[1] Due to its increased awareness and understanding, SIBO is now often considered in most clinician’s differential diagnoses in patients with non-specific gastrointestinal complaints.


The etiology of small intestinal bacterial overgrowth is complex. There are many important host defense mechanisms against bacterial overgrowth. When these protective barriers fail, SIBO occurs. Upon ingestion of food, gastric acids and bile destroy and prevent bacteria from passing through the intestines. Conditions that cause achlorhydria are associated with SIBO.[2] Also, proteolytic enzymes digest and degrade bacteria in the intestines. Chronic pancreatic insufficiency is associated with SIBO.[2] Migrating motor complexes are responsible for peristalsis and cleansing the small intestine.[3] SIBO is associated with disorders of abnormal gastrointestinal motility, such as irritable bowel syndrome, narcotic use, post-radiation enteropathy, hypothyroidism, diabetes mellitus, and scleroderma.[2]

An intact ileocecal valve and antegrade motility prevent retrograde translocation of colonic bacteria.[4] Anatomic abnormalities lead to stasis of the bowels which may predispose to SIBO. Such anatomic disorders may include small intestinal diverticulosis, bowel strictures, post-operative adhesions, gastric bypasses with blind intestinal loops, and ileocecal resection.[2] Lastly, immunoglobin A, which found in abundance in the gastrointestinal tract, also prevents bacterial proliferation and maintains intestinal immunity.[5] Immunodeficiency disorders, such as acquired immune deficiency syndrome, combined variable immunodeficiency, and IgA deficiency, are associated with an increased risk of SIBO.[6]


The actual prevalence of small intestinal bacterial overgrowth is vastly unknown. Disorders of abnormal gastrointestinal motility account for the majority of the cases.[7]


Research has identified multiple species in SIBO. The most common species include Streptococcus, Escherichia coli, Lactobacillus, and Bacteroides.[8] The presence of overabundant bacteria in the small intestines does not always correlate with disease activity. Clinical manifestations only occur when inflammation from invasive strains of bacteria are present.[6] Invasive strains of bacteria can produce enzymes or endotoxins, which damages the epithelial cell layer.[9]

In SIBO, the endoscopic and histopathological appearance of the mucosa is usually healthy. Nonspecific endoscopic changes may include mucosal edema, loss of vascularity, patchy erythema, or rarely ulceration.[10] Nonspecific histopathological findings may consist of villous blunting, cryptitis, intraepithelial lymphocytosis, and eosinophilia.[11]

History and Physical

The clinical manifestations of small intestinal bacterial overgrowth classically include a combination of abdominal discomfort with bloating, flatulence, or chronic watery diarrhea. Steatorrhea and weight loss from fat malabsorption may manifest as well.[12] SIBO causes vitamin deficiencies. Vitamin B12 deficiency occurs from ileal mucosal damage to cobalamin binding sites. Vitamin B1 and B3 deficiencies occur due to bacterial overutilization. In contrast, bacterial synthesis results in the elevation of folate and vitamin K levels.[13]

D-lactic acidosis, a rare neurological syndrome, is characterized by altered mental status, slurred speech, seizures, and ataxia. This syndrome results from bacterial fermentation of unabsorbed carbohydrates. Patients with SIBO associated with short bowel syndrome or a jejunoileal bypass can develop this syndrome.[14] SIBO has been implicated in the development of nonalcoholic fatty liver disease and hepatic encephalopathy.[15] Unless severe malnutrition is evident, physical examination in these patients is generally nonrevealing.


There is no validated gold standard diagnostic test for small intestinal bacterial overgrowth.[1] When a patient is presenting with signs and symptoms concerning for SIBO, the diagnosis garners further support with a positive carbohydrate breath test or a bacterial concentration of more than 1000 colony-forming units/mL in a jejunal aspirate culture.[16] A carbohydrate breath test is a noninvasive, fast, and inexpensive test.[17] The test uses the principle that the metabolism of either lactulose or glucose as its carbohydrate substrate by bacteria will produce either hydrogen or methane. This product will then be absorbed and excreted in the patient’s breath.[16] A rise of more than 20 parts per million from baseline in hydrogen within 90 minutes or a methane level of more than 10 parts per million are positive results.[16]

A jejunal aspirate culture is invasive, time-consuming, and expensive, as it is obtained during an upper endoscopy. The results are also poorly reproducible and can lead to false results from either patchy bacterial overgrowth or contamination with oropharyngeal flora.[18] Other laboratory findings that support a diagnosis of SIBO may include vitamin levels and markers of malnutrition.[12] Once there is a suspicion of SIBO, additional testing in identifying the etiology merit consideration. Anatomic and mucosal abnormalities can be investigated with abdominal imaging and endoscopies. Testing for disorders of abnormal gastrointestinal motility, pancreatic insufficiency, and immunodeficiencies can be considered on a case-by-case basis.[2]

Treatment / Management

The initial mainstay of treatment is the use of antibiotics to eradicate bacterial overgrowth and repletion of any nutritional deficiencies. Metronidazole, ciprofloxacin, tetracycline, amoxicillin-clavulanate, neomycin, and rifaximin are antibiotics used in the treatment, with rifaximin being the most investigated.[19] For patients with hydrogen-predominant bacterial overgrowth, rifaximin 1650 mg/day for two weeks is an effective therapy.[19] For patients with methane-predominant bacterial overgrowth, the combination of neomycin 1000 mg/day and rifaximin 1650 mg/day for two weeks is an effective therapy.[20]

Approximately 45 percent of patients will have recurrent SIBO following completion of antibiotic therapy, with recurrence rates higher in older adults, post-appendectomy, and chronic use of proton pump inhibitors.[21] In patients with early recurrence, within three months, a second course of antibiotics is given. In patients with late recurrence, beyond three months, antibiotics are provided only with positive carbohydrate breath testing. Recurrent SIBO is treatable either with the same initial antibiotic or an alternating antibiotic. If no improvement of symptoms following two courses of treatment, the clinician should consider alternative diagnoses.[22]

Differential Diagnosis

Diagnoses that produce chronic diarrhea should be in the differential and investigated during the evaluation of small intestinal bacterial overgrowth. Irritable bowel syndrome (IBS), celiac disease (CD), and inflammatory bowel disease (IBD) all have considerable overlap with SIBO. Irritable bowel syndrome has recurrent abdominal pain, which is related to bowel movements and associated with a change in stool frequency or appearance.[23] Celiac disease and SIBO have similar clinical symptoms; however, celiac disease will have positive celiac serologies and a negative carbohydrate breath test.[24] Both Crohn disease and SIBO have patchy mucosal inflammation. However, Crohn disease additionally could demonstrate transmural inflammation and granulomas on biopsy and perianal involvement with anal fissures and fistulas.[25]


Prognosis is serious and depends on the etiology of the underlying condition, which is causing small intestinal bacterial overgrowth.[2]


Severe chronic small intestinal bacterial overgrowth can result in significant weight loss and severe malnutrition, which can lead to substantial morbidity and mortality. Early recognition of SIBO can treat the maldigestion of nutrients and prevent malnourishment. If left untreated, SIBO can lead to intestinal failure.[26]


Patients with unexplained chronic diarrhea or signs and symptoms of significant malnutrition should be referred to a gastroenterologist for further evaluation.

Deterrence and Patient Education

Any patients diagnosed with small intestinal bacterial overgrowth should have additional testing to determine etiology and treatment against the underlying condition to prevent recurrent SIBO. Treatment of disorders associated with abnormal intestinal motility, which includes Crohn disease, irritable bowel syndrome, post-radiation enteropathy, diabetes mellitus, hypothyroidism, and scleroderma, should be better optimized and well-controlled. Prokinetics can be useful as adjunctive therapy for these patients.[27] Opioids, which decrease intestinal motility, and proton pump inhibitors, which cause achlorhydria, should be avoided in these patients.[28] Surgical interventions can be a consideration in patients with anatomical abnormalities who have recurrent SIBO.[27] There is limited research on chronic antibiotic prophylaxis, and probiotics have not been shown effective in prevention.[29] However difficult to strictly adhere to, there may be a role for an elemental diet.[30]

Enhancing Healthcare Team Outcomes

Small intestinal bacterial overgrowth is an under-recognized condition with significant morbidity and mortality. Optimal management of SIBO is by an interprofessional team of primary care physicians, gastroenterologists, surgeons, dieticians, pharmacists, and nurses. Early recognition leads to more favorable outcomes and can prevent severe malnutrition. Once SIBO is diagnosed, and the patient is on antibiotics, further management should be directed at the treatment of the underlying etiology to prevent further recurrences.

During initial treatment, nursing should be vigilant in monitoring treatment effectiveness and progress, as well as verifying patient compliance. The patient’s calorie intake and weight assessments should be frequently monitored during and after treatment to ensure adequate recovery from their illness. Nursing should follow all these areas and report back to the treating physician with any concerns. The pharmacist can assist with agent selection, verification of dosing parameters, and performing medication reconciliation. The pharmacist should also work directly with the clinician and nurse regarding potential drug-condition interactions (e.g., opioids, PPIs). SIBO management requires an interprofessional team approach, including physicians, specialists, specialty-trained nurses, and pharmacists, all collaborating across disciplines to achieve optimal patient results. [Level 5] The overall outcome is dependent on the management of the underlying condition. If the etiology is not well managed, the overall prognosis is grave.[2] [Level 2]

Review Questions


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Bookshelf ID: NBK546634PMID: 31536241


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